Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data

Marissa Kaminski; Joshua I Brown; Sara R Seibert; Flor Hernández; Melizar V Duya; Ian Kendrich C Fontanilla; David Roshier; Adam Miles; Leo Joseph; Jeffrey L Peters; Philip Lavretsky

doi:10.1016/j.ympev.2024.108085

Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data

Mol Phylogenet Evol. 2024 Apr 28:108085. doi: 10.1016/j.ympev.2024.108085. Online ahead of print.

Authors

Affiliations

¹ Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA. Electronic address: mkaminski@usgs.gov.
² Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA.
³ Department of Biological Sciences, Wright State University, Dayton, OH, USA.
⁴ Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines.
⁵ School of Animal and Veterinary Science, University of Adelaide, Roseworthy SA, Australia.
⁶ Department of Marine and Wildlife Resources, Pago Pago American 96799, Samoa.
⁷ Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia.

PMID: 38688441
DOI: 10.1016/j.ympev.2024.108085

Abstract

Aim: We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines.

Location: Oceania, greater Indonesia, and the Philippines.

Taxon: Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species.

Results: Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Tasmania, Papua New Guinea, and Timor-Leste. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples.

Main conclusions: Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.

Keywords: Anas; Conservation; Evolution; Phylogenetics; Population genetics.